Showing : scrnaseq • reset
5
votes
13
replies
1.1k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 5 weeks ago by 53k • written 7 weeks ago by • 0
0
votes
1
reply
166
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
9 weeks ago • updated 8 weeks ago Francesco Silvestro • 0
1
vote
10
replies
1.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 5 weeks ago by • 0 • written 10 weeks ago by • 0
1
vote
2
replies
311
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 11 weeks ago by 53k • written 11 weeks ago by • 0
0
votes
11
replies
868
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
12 weeks ago • updated 11 weeks ago Peter Hickey ▴ 760
0
votes
3
replies
936
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
0
replies
359
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
8 months ago Muhammad • 0
0
votes
3
replies
828
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 9 months ago by • 0 • written 9 months ago by ▴ 10
2
votes
2
replies
813
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 14 months ago by ▴ 10
0
votes
0
replies
746
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
16 months ago Damini • 0
1
vote
8
replies
1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 16 months ago by 53k • written 16 months ago by • 0
0
votes
0
replies
618
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
17 months ago Bibi • 0
0
votes
1
reply
950
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 18 months ago by ★ 5.0k • written 19 months ago by • 0
0
votes
2
replies
1.0k
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
19 months ago rocanja ▴ 60
0
votes
1
reply
721
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
vote
2
replies
1.9k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
23 months ago ruba-mahmoud • 0
0
votes
2
replies
1.4k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.1 years ago Momo • 0
0
votes
1
reply
837
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
votes
5
replies
1.8k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.2 years ago duez.tolga • 0
0
votes
1
reply
2.8k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
4
votes
3
replies
1.7k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
0
votes
1
reply
911
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
959
views
library(topGO) query
topGO scRNAseq
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
0
votes
0
replies
769
views
adding noise to scRNA Seq counts
scRNAseq
2.3 years ago Jiyuan • 0
1
vote
11
replies
9.4k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 24 months ago by • 0 • written 2.3 years ago by • 0
2
votes
3
replies
2.1k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.4 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
1.0k
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
2.4 years ago info ▴ 10
0
votes
1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.5 years ago by 4.2k • written 2.5 years ago by ★ 1.6k
2
votes
0
replies
2.5k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.6 years ago Tadeoye ▴ 20
0
votes
1
reply
1.5k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by ▴ 10
4
votes
5
replies
2.9k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 2.0 years ago by • 0 • written 2.7 years ago by • 0
0
votes
3
replies
2.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 15 months ago by • 0 • written 3.0 years ago by • 0
1
vote
2
replies
2.0k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
3.1 years ago • updated 3.0 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.5k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.1 years ago • updated 3.0 years ago evocanres • 0
0
votes
3
replies
1.7k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.1 years ago Madiha • 0
4
votes
5
replies
4.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.2 years ago Peter Hickey ▴ 760
4
votes
2
replies
1.8k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.2 years ago Guandong Shang ▴ 40
0
votes
4
replies
3.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.2 years ago by ★ 29k • written 3.3 years ago by ▴ 40
0
votes
0
replies
1.4k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.3 years ago peter.kharchenko ▴ 30
0
votes
0
replies
1.1k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.3 years ago Sebastian Lewandowski • 0
1
vote
4
replies
2.0k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.3 years ago Chise ▴ 10
0
votes
0
replies
1.6k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.3 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.7k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
votes
1
reply
1.7k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
votes
8
replies
2.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.4 years ago • updated 3.3 years ago Kelen ▴ 10
0
votes
1
reply
1.1k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
1
vote
2
replies
3.0k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.5 years ago Ismail • 0
1
vote
1
reply
2.9k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.6 years ago by ▴ 760 • written 3.6 years ago by • 0
2
votes
2
replies
2.1k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.7 years ago behr201 • 0
95 results • Page 1 of 2
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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